Stronger preference of human tumor suppressor protein BRCA1 for an open-planar Holliday junction: Insights from a...

BRCA1 is a complex tumor suppressor protein involved in multiple critical cellular processes, e.g., DNA double-strand break repair, cell cycle checkpoint, etc. BRCA1-depleted cells show decreased homologous recombination (HR) and promote error-prone non-homologous end joining for DNA damage repair. Holliday junction (HJ) is an essential intermediate of DNA damage repair mechanism through HR. BRCA1 protein has high affinity for HJ and recruits several proteins to DNA damage site. Nonetheless, questions remain regarding the binding of BRCA1 protein with HJ. Does BRCA1 protein show preference for isomers of HJ? Why do specific mutations in BRCA1 protein lead to impaired DNA damage repair? Do those amino acids play any role in BRCA1-HJ interactions? Using single-molecule Fluorescence Correlation Spectroscopy, we showed that BRCA1 prefers an open-planar conformation of HJ and has a 10-fold lesser affinity for stacked HJ. The preference for an open-planar structure is independent of the nucleotide sequence at the branch point. Molecular docking and all-atom molecular dynamics simulation unraveled that primarily charged and polar residues in the DNA binding region from exon 11 of BRCA1 participated in the interaction. Most of those amino acids are places for missense changes. Further computational studies revealed that mutating these residues disrupted the interaction.